Although enhanced structural relaxation is generally believed to be an important contributor to the work hardening of metallic glasses subjected to a triaxial stress state, direct observation of the relaxation process in response to work hardening has not been achieved in metallic glasses. Here, we show that nanoscratching an atomically flat bulk metallic glass surface, a small atomic force microscopy tip with a radius of ~10 nm, results in a high hydrostatic stress within the stressed volume. This enables densifying plastic flow via enhanced structural relaxation and leads to work hardening behavior, as evidenced by an obvious decrease in friction force signals within scratched regions. Further examination of the atomic structure beneath the scratched surface via high-resolution transmission electron microscopy reveals a relaxed structural configuration, which is indicated by dispersed clusters of medium-range order scale in the case of line scratching and nucleated nanocrystals in the case of cyclic scratching. This study provides compelling evidence for stress-driven structural relaxation, greatly deepening the understanding of the work-hardening mechanism in metallic glasses.